Atheism isn't a belief system but, rather, a lack thereof.
Perhaps the reason atheists are more likely to be vegans is because they do not have the specific belief that God made these other animals to be eaten.
Perhaps a lot of religious people have a gut feeling that eating animals isn't right, but they are consoled by the belief that God made these animals specifically to be eaten by humans.
That said, it's possible to be an atheist who believes that we are omnivores and that us eating meat is no more morally wrong than dogs eating meat or bears eating meat, etc. But a religious person could have that reason, too, for not being a vegan.